My software notes

January 27, 2011

Names of Atoms of Amino acids

Filed under: softwares and scripts,xplor/xplor-nih/cns — kpwu @ 4:03 pm
Tags: ,

I really hate the inconsistent nomenclature of atoms of amino acids between different programs/database. I finished all NOESY assignment on Sparky using PDB nomenclature and the Sparky XPLOR constraint plugin (shortcut xf) doesn’t take care of the differences between XPLOR and PDB. Thus I have to find a table showing me the differences of names between XPLOR and PDB.

I found BMRB provides such table including few programs (XPLOR, DIANA, PDB, BMRB, SYBYL…) and I have extracted the BMRB/PDB/XPLOR/DIANA columns and reorganized the information. The new table I made is saved as PDF and attached.

Snapshot of part of this table is shown here.

Attached PDF: AA_atoms-nomemclature



  1. Hi,

    I am a great follower of your posts. The information mentioned in your posts , I found very valuable in field of structural biology. I have one query regarding your experience with Sparky and Xplor-NIH. I am using ARIA2.2 which is similar like Xplor-NIH. Have u tried assigning your N15Edit NOESY and C13 Edit NOESY peak list from the NOESY assignment done by ARIA2.2


    Comment by Arun — October 25, 2012 @ 10:37 pm | Reply

    • Hi Arun,

      Unfortunately, I met problems installing Aria 2.2 previously on my iMac. What I remember is that Aria2.2 requires a bunch of external programs and some of them (e.g Tix 8.1.4) were not successfully installed on my iMac either using Fink or Ports. I’d love to try thew newest Aria if it’s less painful to be installed on Mac OS X. Last time I have used Aria was version 1.0 9 years ago! I believe you can find some experienced users around your university.

      Comment by kpwu — October 25, 2012 @ 11:27 pm | Reply

  2. Hi,

    I am working on a protein which is all helix as secondary structure. I want to compare changes happening in the inter helical angles when this protein interacts with other protein. Can you suggest some online software which can provide this information or can Pymol provide this kind of information.



    Comment by Arun — November 13, 2012 @ 8:56 pm | Reply

  3. Hi,

    I have come across a peculiar problem . I have generated a docking model of heterotetrameric complex from HADDOCK. I got best 20 structures which I want to deposit as ensemble file for PDB deposition. Before I can observe secondary structure for each model pdb in Pymol. When I copied all model 1-20 pdbs to one pdb, now suddenly each model in ensemble pdb is looking like random coil. But in Molmol, I still can observe the secondary structure of ensemble PDBs. Can you suggest way to overcome this problem in Pymol



    Comment by Arun — November 30, 2012 @ 9:01 am | Reply

    • Perhaps asking at HADDOCK forum or PyMOL forum is a better solution to you.

      I would try “dss” command in pymol.

      Comment by kpwu — November 30, 2012 @ 10:20 pm | Reply

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